Metafusion.clinical.sh not accounting for options in file naming.

[pintoa1-mskcc]

There are a few times within the Metafusion.clinical.sh script where if an option isnt specified, the name of the file is still updated and results in an empty file and failure for the rest of the run

1. MetaFusion-Clinical/scripts/MetaFusion.clinical.sh

   Line 162 in f29363c

   cluster=$outdir/$(basename $cff).isoforms.per_sample.cluster

2. MetaFusion-Clinical/scripts/MetaFusion.clinical.sh

   Line 169 in f29363c

   cluster=$outdir/$(basename $cluster).non_hgnc_removed

3. MetaFusion-Clinical/scripts/MetaFusion.clinical.sh

   Line 181 in f29363c

   cluster=$outdir/$(basename $cluster).cancer_db_hits

4. etc etc...

[mapostolides]

Is this a breaking bug, or can you still use the tool by specifying the flag? Which specific flag are you referring to?

[pintoa1-mskcc]

Not including per sample, pfam or fusion annotator breaks the function, as well as in the locations listed. I commented out those sections to allow it to run, but i saw this occurring in multiple locations where the cluster filename was specified outside the if statement of the flag. Any "optional" flag shouldnt have the cluster name being updated outside the if statement